From 294349b1dd2e8bfa00eb8f1932d0f6404b2600b8 Mon Sep 17 00:00:00 2001 From: "W. Trevor King" Date: Wed, 8 May 2013 22:36:07 -0400 Subject: [PATCH] Convert existing external references to \xref, \fref, etc. Hooray consistency! --- src/apparatus/polymer-synthesis.tex | 6 +- src/blurb/gumbel.tex | 4 +- src/calibcant/main.bib | 18 +---- src/calibcant/theory.tex | 8 +- src/root.bib | 117 +++++++++++++++++++++------- src/sawsim/conclusions.tex | 20 ++--- src/sawsim/discussion.tex | 4 +- src/viscocity/main.tex | 15 ++-- 8 files changed, 121 insertions(+), 71 deletions(-) diff --git a/src/apparatus/polymer-synthesis.tex b/src/apparatus/polymer-synthesis.tex index 1fca013..29cbe10 100644 --- a/src/apparatus/polymer-synthesis.tex +++ b/src/apparatus/polymer-synthesis.tex @@ -85,9 +85,9 @@ is\citep{carrion-vazquez99b} \begin{figure} \includegraphics[width=0.9\textwidth]{figures/binary/kempe85-fig2}% - \caption{Example of gene duplication via plasmid splicing (Figure~2 - from \citet{kempe85}). \citet{kempe85} use a different gene, but - some of the restriction enzymes are shared with + \caption{Example of gene duplication via plasmid splicing + (\xref{kempe85}{figure}{2}). \citet{kempe85} use a different + gene, but some of the restriction enzymes are shared with \citet{carrion-vazquez99b}. The overall approach is identical.\label{fig:plasmid}} \end{figure} diff --git a/src/blurb/gumbel.tex b/src/blurb/gumbel.tex index 97189b1..2b9ae38 100644 --- a/src/blurb/gumbel.tex +++ b/src/blurb/gumbel.tex @@ -71,5 +71,5 @@ the older and equivalent Gompertz distribution\citep{gompertz25,olshansky97,wu04}. eq:sawsim:order-depA warning about the ``Gompertz'' model is in order, because there seem to be at least two unfolding/dying rate formulas that go by that name. -Compare, for example, \citet{braverman08} Eqn.~5 and \citet{juckett93} -Fig.~2.}, +Compare, for example, \xref{braverman08}{equation}{5} and +\xref{juckett93}{figure}{2}. diff --git a/src/calibcant/main.bib b/src/calibcant/main.bib index 6ee65ef..fdc4671 100644 --- a/src/calibcant/main.bib +++ b/src/calibcant/main.bib @@ -15,7 +15,7 @@ crossref = "thornton04", chapter = "Appendix D", pages = 609, - note = "See Eq.~12.0.13", + note = "See \fref{equation}{12.0.13}", } @@ -32,21 +32,21 @@ crossref = "press92", chapter = 12, pages = 498, - note = "See Eq.~12.0.13", + note = "See \fref{equation}{12.0.13}", } @Inbook{PSD, crossref = "press92", chapter = 12, pages = 498, - note = "See Eq.~12.0.14", + note = "See \fref{equation}{12.0.14}", } @Inbook{wiener-khinchin, crossref = "press92", chapter = 12, pages = 498, - note = "See Eq.~12.0.12", + note = "See \fref{equation}{12.0.12}", } @Misc{wikipedia-wiener-khinchin, @@ -57,13 +57,3 @@ month = "TODO", year = "TODO", } - -@Misc{tweezer-lab-notes, - author = "C.\ Grossman and A.\ Stout", - title = "Optical Tweezers Advanced Lab", - month = "Fall", - year = "2005", - note = "See section 4.3", -} -% \url{http://chirality.swarthmore.edu/PHYS81/OpticalTweezers.pdf} -% \url{http://nlolab.swarthmore.edu/webstuff/Phys81_82/OpticalTweezersLabTheory.pdf} diff --git a/src/calibcant/theory.tex b/src/calibcant/theory.tex index 6baa1a6..4939cd0 100644 --- a/src/calibcant/theory.tex +++ b/src/calibcant/theory.tex @@ -169,10 +169,10 @@ Plugging \cref{eq:ODHO-var} into \cref{eq:equipart} we have Combining \cref{eq:ODHO-psd-GO,eq:ODHO-GO}, we expect $x(t)$ to have a power spectral density per unit time given by\footnote{% - \cref{eq:ODHO-psd} is Eq.~(A12) from \citet{bechhoefer02} (who's + \cref{eq:ODHO-psd} is \xref{bechhoefer02}{equation}{A12} (who's $\tau_0\equiv\gamma/\kappa$), except that they're missing a factor of $1/\pi$. - \cref{eq:ODHO-psd} is also Eq.~(8) from \citet{burnham03}, where + \cref{eq:ODHO-psd} is also \xref{burnham03}{equation}{8}, where their damping coefficient $b$ is equivalent to our $\gamma$, their frequency $\nu$ is equivalent to our $f=\omega/2\pi$, and their roll off frequency $\nu_R\equiv k/2\pi b$ is equivalent to our @@ -270,7 +270,7 @@ Plugging \cref{eq:DHO-var} into the equipartition theorem Combining \cref{eq:model-psd,eq:GO}, we expect $x(t)$ to have a power spectral density per unit time given by\footnote{% - \cref{eq:DHO-psd} is Eq.~(8.11) from \citet{benedetti12}. + \cref{eq:DHO-psd} is \xref{benedetti12}{equation}{8.11}. } \begin{equation} \PSD(x, \omega) = \frac{2 k_BT \beta} @@ -426,7 +426,7 @@ Plugging \cref{eq:Gone-f} into \cref{eq:psd-Vp}, we have \PSD_f(V_p, f) = \frac{\sigma_p^2 k_BT \beta_f}{2\pi^3 m} \cdot \frac{1}{(f_0^2-f^2)^2 + \beta_f^2 f^2} \end{equation} -From which we can recover \citet{burnham03}'s Eq.~(6). +From which we can recover \xref{burnham03}{equation}{6}. \begin{align} \PSD_f(x, f) &= \frac{\PSD_f(V_p, f)}{\sigma_p^2} = \frac{k_BT \colA{\beta_f}}{2\pi^3 m} \cdot diff --git a/src/root.bib b/src/root.bib index 0c2d785..8d04f80 100644 --- a/src/root.bib +++ b/src/root.bib @@ -279,6 +279,7 @@ @string{HErickson = "Erickson, Harold P."} @string{MEsaki = "Esaki, Masatoshi"} @string{SEsparham = "Esparham, S."} +@string{EBJ = "European biophysics journal: EBJ"} @string{EJP = "European Journal of Physics"} @string{EPL = "Europhysics Letters"} @string{CEvangelista = "Evangelista, C."} @@ -705,7 +706,7 @@ @string{VMoy = "Moy, Vincent T."} @string{SMukamel = "Mukamel, Shaul"} @string{DJMuller = "M{\"u}ller, Daniel J."} -@string{PMundel = "Mundel, P."} +@string{PMundel = "Mundeol, P."} @string{EMuneyuki = "Muneyuki, Eiro"} @string{RJMural = "Mural, R. J."} @string{BMurphy = "Murphy, B."} @@ -3295,9 +3296,10 @@ of the oscillator's amplitude fluctuations. We evaluate this method in comparison to the three others and recommend it for its ease of use and broad applicability.}, - note = {Contains both the overdamped (Eq.~6) and general (Eq.~8) - power spectral densities used in thermal cantilever calibration, - but punts to textbooks for the derivation.}, + note = {Contains both the overdamped (\fref{equation}{6}) and + general (\fref{equation}{8}) power spectral densities used in + thermal cantilever calibration, but punts to textbooks for the + derivation.}, } @article { forde02, @@ -3634,14 +3636,16 @@ season = "Fall", numpages = 12, eprint = "http://chirality.swarthmore.edu/PHYS81/OpticalTweezers.pdf", - note = "Fairly complete overdamped PSD derivation in section 4.3., cites - \citet{tlusty98} and \citet{bechhoefer02} for further details. However, - Tlusty (listed as reference 8) doesn't contain the thermal response - fn.\ derivation it was cited for. Also, the single sided PSD definition - credited to reference 9 (listed as Bechhoefer) looks more like Press - (listed as reference 10). I imagine Grossman and Stout mixed up their - references, and meant to refer to \citet{bechhoefer02} and - \citet{press92} respectively instead.", + note = {Fairly complete overdamped PSD derivation in + \fref{section}{4.3}. Cites \citet{tlusty98} and + \citet{bechhoefer02} for further details. However, Tlusty + (listed as reference 8) doesn't contain the thermal response + fn.\ derivation it was cited for. Also, the single sided PSD + definition credited to reference 9 (listed as Bechhoefer) + looks more like Press (listed as reference 10). I imagine + Grossman and Stout mixed up their references, and meant to + refer to \citet{bechhoefer02} and \citet{press92} respectively + instead.}, project = "Cantilever Calibration" } @@ -3889,7 +3893,7 @@ mechanical unfolding experiments of proteins and RNA, the ruggedness energy scale epsilon, can be directly measured.", note = "Derives the major theory behind my thesis. The Kramers rate - equation is \citet{hanggi90} Eq.~4.56c (page 275).", + equation is \xref{hanggi90}{equation}{4.56c} (page 275).", project = "Energy Landscape Roughness" } @@ -5574,8 +5578,9 @@ allowed us to map the features of the complex energy landscape of GFP including a characterization of the structures, albeit at a coarse- grained level, of the three metastable intermediates.", - note = "Hiccup in unfolding leg corresponds to unfolding intermediate (See - Figure 2). The unfolding timescale in GFP is about 6 ms." + note = {Hiccup in unfolding leg corresponds to unfolding + intermediate (\fref{figure}{2}). The unfolding timescale in GFP + is about $6\U{ms}.} } @article { nevo03, @@ -6156,7 +6161,7 @@ publisher = CUP, address = "New York", eprint = "http://www.nrbook.com/a/bookcpdf.php", - note = "See sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to + note = "See Sections 12.0, 12.1, 12.3, and 13.4 for a good introduction to Fourier transforms and power spectrum estimation.", project = "Cantilever Calibration" } @@ -6203,12 +6208,13 @@ shown with bacteriorhodopsin and with protein constructs containing GFP and titin kinase.", note = {Contour length space and barrier position fingerprinting. - There are errors in Eq.~(3), propagated from \citet{livadaru03}. - I contacted Elias Puchner and pointed out the typos, and he - revised his FRC fit parameters from $\gamma=22\dg$ and - $b=0.4\U{nm}$ to $\gamma=41\dg$ and $b=0.11\U{nm}$. The combined - effect on Fig.~(3) of fixing the equation typos and adjusting the - fit parameters was small, so their conclusions are still sound.}, + There are errors in \fref{equation}{3}, propagated from + \citet{livadaru03}. I contacted Elias Puchner and pointed out the + typos, and he revised his FRC fit parameters from $\gamma=22\dg$ + and $b=0.4\U{nm}$ to $\gamma=41\dg$ and $b=0.11\U{nm}$. The + combined effect on \fref{figure}{3} of fixing the equation typos + and adjusting the fit parameters was small, so their conclusions + are still sound.}, } @article { raible04, @@ -6701,16 +6707,17 @@ beyond the Bell model.", note = {The inspiration behind my sawtooth simulation. Bell model fit to $f_{unfold}(v)$, but Kramers model fit to unfolding - distribution for a given $v$. Eqn.~3 in the supplement is - \citet{evans99} 1999's Eqn.~2, but it is just + distribution for a given $v$. \fref{equation}{3} in the + supplement is \xref{evans99}{equation}{2}, but it is just $[\text{dying percent}] \cdot [\text{surviving population}] = [\text{deaths}]$. $\nu \equiv k$ is the force/time-dependent off rate. The Kramers' rate equation (on page L34, the second equation in the paper) is - \citet{hanggi90} Eq.~4.56b (page 275) and \citet{socci96} Eq.~2, - but \citet{schlierf06} gets the minus sign wrong in the exponent. - $U_F(x=0)\gg 0$ and $U_F(x_\text{max})\ll 0$ (\cf~Schlierf's - Fig.~1). Schlierf's integral (as written) contains + \xref{hanggi90}{equation}{4.56b} (page 275) and + \xref{socci96}{equation}{2} but \citet{schlierf06} gets the minus + sign wrong in the exponent. $U_F(x=0)\gg 0$ and + $U_F(x_\text{max})\ll 0$ (\cf~\xref{schlierf06}{figure}{1}). + Schlierf's integral (as written) contains $\exp{-U_F(x_\text{max})}\cdot\exp{U_F(0)}$, which is huge, when it should contain $\exp{U_F(x_\text{max})}\cdot\exp{-U_F(0)}$, which is tiny. For more details and a picture of the peak that @@ -8563,6 +8570,55 @@ note = {Development stalled in 2005 after Michael graduated.}, } +@article{ janovjak05, + author = HJanovjak #" and "# JStruckmeier #" and "# DJMuller, + title = {Hydrodynamic effects in fast {AFM} single-molecule + force measurements.}, + year = 2005, + month = feb, + day = 15, + address = {BioTechnological Center, University of Technology + Dresden, 01307 Dresden, Germany.}, + journal = EBJ, + volume = 34, + number = 1, + pages = {91--96}, + issn = {0175-7571}, + doi = {10.1007/s00249-004-0430-3}, + url = {http://www.ncbi.nlm.nih.gov/pubmed/15257425}, + language = {eng}, + keywords = {Algorithms}, + keywords = {Computer Simulation}, + keywords = {Elasticity}, + keywords = {Microfluidics}, + keywords = {Microscopy, Atomic Force}, + keywords = {Models, Chemical}, + keywords = {Models, Molecular}, + keywords = {Physical Stimulation}, + keywords = {Protein Binding}, + keywords = {Proteins}, + keywords = {Stress, Mechanical}, + keywords = {Viscosity}, + abstract = {Atomic force microscopy (AFM) allows the critical forces + that unfold single proteins and rupture individual receptor-ligand + bonds to be measured. To derive the shape of the energy landscape, + the dynamic strength of the system is probed at different force + loading rates. This is usually achieved by varying the pulling + speed between a few nm/s and a few $\mu$m/s, although for a more + complete investigation of the kinetic properties higher speeds are + desirable. Above 10 $\mu$m/s, the hydrodynamic drag force acting + on the AFM cantilever reaches the same order of magnitude as the + molecular forces. This has limited the maximum pulling speed in + AFM single-molecule force spectroscopy experiments. Here, we + present an approach for considering these hydrodynamic effects, + thereby allowing a correct evaluation of AFM force measurements + recorded over an extended range of pulling speeds (and thus + loading rates). To support and illustrate our theoretical + considerations, we experimentally evaluated the mechanical + unfolding of a multi-domain protein recorded at $30\U{$mu$m/s} + pulling speed.}, +} + @article{ sandal09, author = MSandal #" and "# FBenedetti #" and "# MBrucale #" and "# AGomezCasado #" and "# BSamori, @@ -9965,7 +10021,8 @@ might help to resolve the discrepancies encountered when trying to fit experimental data for the stretching response of polymers in a broad force range with a single effective persistence length.}, - note = {There are two typos in Eq.~(46). \citet{livadaru03} have + note = {There are two typos in \fref{equation}{46}. + \citet{livadaru03} have \begin{equation} \frac{R_z}{L} = \begin{cases} \frac{fa}{3k_BT} & \frac{fb}{k_BT} < \frac{b}{l} \\ @@ -9988,7 +10045,7 @@ along with the fact that even with the corrected formula there is a discontinuity between the low- and moderate-force regimes. Netz confirmed the errors, and pointed out that the discontinuity is - because Eq.~(46) only accounts for the scaling (without + because \fref{equation}{46} only accounts for the scaling (without prefactors). Unfortunately, there does not seem to be a published erratum pointing out the error and at least \citet{puchner08} have quoted the incorrect form.}, diff --git a/src/sawsim/conclusions.tex b/src/sawsim/conclusions.tex index 60fe984..b4551e5 100644 --- a/src/sawsim/conclusions.tex +++ b/src/sawsim/conclusions.tex @@ -4,12 +4,14 @@ We have described the method of performing Monte Carlo simulations based on a simple two-state model for the mechanical unfolding of protein molecules and discussed the complications involved in the -simulation procedure. In addition to the extraction of kinetic -properties of the protein from mechanical unfolding data, such -simulations can help to elucidate the effects of various experimental -parameters on the appearance of force curves and to estimate the -errors associated with data pooling. To date, the force-induced -unfolding approach has been used to investigate several different -types of proteins. As the technique is used to study a wider range of -proteins, this simple simulation method will be useful for data -analysis, experimental design, and artifact identification. +simulation procedure. Besides its use in this thesis, +\sawsim\ analysis has been used in \xref{roman12}{figure}{75}. In +addition to the extraction of kinetic properties of the protein from +mechanical unfolding data, such simulations can help to elucidate the +effects of various experimental parameters on the appearance of force +curves and to estimate the errors associated with data pooling. To +date, the force-induced unfolding approach has been used to +investigate several different types of proteins. As the technique is +used to study a wider range of proteins, this simple simulation method +will be useful for data analysis, experimental design, and artifact +identification. diff --git a/src/sawsim/discussion.tex b/src/sawsim/discussion.tex index 7c3747d..e2fde92 100644 --- a/src/sawsim/discussion.tex +++ b/src/sawsim/discussion.tex @@ -61,8 +61,8 @@ low-dimensional parameter spaces). parameters are those given by \citet{carrion-vazquez99b}. \citet{carrion-vazquez99b} don't list their cantilever spring constant (or, presumably, use it in their simulations), but we - can estimate it from the rebound slope in their Figures~2.a and - 2.b, see + can estimate it from the rebound slope in their + \fref{figure}{2.a} and \iref{figure}{2.b}, see \cref{fig:sawsim:kappa-sawteeth}.\label{tab:sawsim:model}} \end{center} \end{table} diff --git a/src/viscocity/main.tex b/src/viscocity/main.tex index 7db3c8d..99ea2b9 100644 --- a/src/viscocity/main.tex +++ b/src/viscocity/main.tex @@ -5,7 +5,8 @@ {\Large M\"uller notes} \\ \end{center} -We had some trouble with their notation, so I'll try and clear some things up... +We had some trouble with the notation in \citet{janovjak05}, so I'll +try and clear some things up\ldots \begin{center} \begin{tabular}{r|l|l} @@ -36,29 +37,29 @@ M\"uller equations: \end{align} Trevor derivations: \\ -For Eqn. \ref{mul_delF}, we assume that all the fluid in the cell moves with the surface +For \cref{mul_delF}, we assume that all the fluid in the cell moves with the surface (i.e., fluid flow does not depend on height above the surface). So the drag force is proportional to the speed of the tip relative to the surface. \begin{equation} F_d = D(h) v_{tip,surface} \end{equation} Where $D(h)$ is some constant that can depend on $h$ (like $6 \pi \eta a_{eff}^2 / (h + d_{eff})$). -This is M\"uller Eqn \ref{mul_Fd}. +This is \xref{janovjak05}{equation}{mul\_Fd??}. Substituting in $v_{tip,surface} = v_{eq,surface} - v_{tip,eq}$ we have \begin{align} F_d &= D(h) v_{eq,surface} - D(h)v_{tip,eq} = F_{d:eq,surface} - F_{d:tip,eq} \\ F_{d:tip, eq} &= F_{d:eq,surface} - F_d \end{align} -This is M\"uller Eqn \ref{mul_delF}. +This is \xref{janovjak05}{equation}{mul\_delF??}. The measured force deflecting the cantilever is then \begin{align} F_{measured} &= F_{protein} + F_d \\ F_{protein} &= F_{measured} - F_d = F_{measured} - (F_{d:eq,surface} - F_{d:tip,eq}) \\ &= F_{meas,zeroed}' + F_{d:tip,eq} = F_{meas,zeroed}' + D(h)v_{tip,eq} \end{align} -This is M\"uller Eqn \ref{mul_Fnet}. +This is \xref{janovjak05}{equation}{mul\_Fnet??}. -The treatment assumes the drag force on a detached cantilever doesn't depend on distance (see dashed line in Figure 4b,c), which doesn't make sense because +The treatment assumes the drag force on a detached cantilever doesn't depend on distance (see dashed line in \xref{janovjak05}{figure}{4b,c}), which doesn't make sense because \begin{equation} F_{d:eq,surface} = D(h)v_{eq,surface} \end{equation} @@ -69,7 +70,7 @@ And $D(h)$ depends on $h$. Therefore, this treatment uses $F_{meas,zeroed}'$, n \end{equation} What can we do about this? -The correction from $F_{meas,zeroed}'$ (solid line in Figure 3a) to $F_{protein}$ (dashed line) comes from adding $F_{d:tip,eq}$, which is why $F_{protein} = F_{meas,zeroed}'$ when +The correction from $F_{meas,zeroed}'$ (solid line in \xref{janovjak05}{figure}{3a}) to $F_{protein}$ (dashed line) comes from adding $F_{d:tip,eq}$, which is why $F_{protein} = F_{meas,zeroed}'$ when \begin{align} 0 = F_{d:tip,eq} \propto v_{tip,eq} = \frac{dz_{cantilever}}{dt} \propto \frac{dF_{meas,zeroed}}{dt}, \\ \end{align} -- 2.26.2